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User talk:Jarlemag
From 2012.igem.org
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| - | ===Useful links=== | + | =Tasks= |
| + | |||
| + | *Make cloramphenicol stock. Check. | ||
| + | *Make glycerol stocks of important parts. Discard old plates. Check. | ||
| + | *Perform CFU-assay of lysis induced cells. Check. Redo? | ||
| + | *Combine LuxR-HSL and lysis device. | ||
| + | *Combine pBAD and GFP | ||
| + | |||
| + | *Research lactate production in E. coli | ||
| + | *Write more for the book chapter | ||
| + | *Research QuikChange | ||
| + | |||
| + | |||
| + | ==Useful links== | ||
| + | |||
| + | http://www.nanodrop.com/Support.aspx?Type=Maintenance&Cat=NanoDrop%201000 | ||
| + | |||
| + | http://www.troemner.com/pdf/PipetteStandardsHandbook.pdf' | ||
| + | |||
| + | http://www.pipette.com/Support/GuideToPipetting.pdf | ||
| + | |||
| + | |||
| + | https://2008.igem.org/Team:EPF-Lausanne/2-step_PCR | ||
| + | |||
| + | https://2009.igem.org/Team:UNIPV-Pavia/Parts_Characterization#Microplate_reader_experiments | ||
| + | |||
| + | [http://www.jbioleng.org/content/5/1/17 Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits] | ||
| + | |||
| + | [http://www.sbkb.org/tt/ Structural Biology Target Registration Database] | ||
| + | |||
| + | [http://dnasu.asu.edu/DNASU/ DNASU plasmid repository] | ||
| + | |||
| + | [http://www.addgene.org/ Addgene plasmid repository] | ||
| + | |||
| + | [http://plasmid.med.harvard.edu/PLASMID/ PlasmID database] | ||
| + | |||
| + | |||
| + | [http://www.chuq.qc.ca/labomoss/english%20pages/protocols.html Moss lab protocols] | ||
| + | |||
| + | ===Lactate genes and promoters:=== | ||
| + | |||
| + | [http://www.biomedcentral.com/1471-2180/10/321#B24 Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate] | ||
| + | |||
| + | [http://aem.asm.org/content/71/10/5920.full Characterization of a Corynebacterium glutamicum Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production†] | ||
| + | |||
| + | [http://www.genome.jp/dbget-bin/www_bget?cgb:cg1027 KEGG: cg1027] | ||
| + | |||
| + | [http://jb.asm.org/content/191/13/4251.abstract The ldhA Gene, Encoding Fermentative l-Lactate Dehydrogenase of Corynebacterium glutamicum, Is under the Control of Positive Feedback Regulation Mediated by LldR | ||
| + | |||
| + | [http://mic.sgmjournals.org/content/142/5/1297 Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif] | ||
| + | |||
| + | [http://www.sciencedirect.com/science/article/pii/S016816560300155X Promoters of Corynebacterium glutamicum] | ||
| + | |||
| + | [http://www.rcsb.org/pdb/explore/explore.do?structureId=2di3 C. glutamicum lldR crystal structure] | ||
| + | |||
| + | |||
| + | RNA polymerase: | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/9916034 Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study] | ||
| + | |||
| + | [http://pubs.acs.org/doi/abs/10.1021/jp9071197 Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner] | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/10910724 Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase] | ||
| + | |||
| + | [http://www.sciencedirect.com/science/article/pii/0092867495903879 Wang et al, 1995: Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex] | ||
==DNA oligo and gene synthesis== | ==DNA oligo and gene synthesis== | ||
| Line 27: | Line 91: | ||
http://molbiol-tools.ca/molecular_biology_freeware.htm | http://molbiol-tools.ca/molecular_biology_freeware.htm | ||
| + | |||
| + | |||
| + | ==quorum sensing== | ||
| + | |||
| + | [http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.165 Quorum sensing in bacteria - Annu. Rev. Microbiol. 2001. 55:165–99] | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed/16487323 N-acyl-L-homoserine lactone signal interception by Escherichia coli.] | ||
| + | |||
| + | |||
| + | |||
| + | ==Other== | ||
| + | |||
| + | [http://www.bion.no/2011/11/syntetisk-biologi/ Syntetisk biologi: Genmodifisert bakterie drep annan bakterie] | ||
| + | |||
| + | http://en.wikipedia.org/wiki/DNA_ligase | ||
Latest revision as of 19:04, 24 July 2012
Contents |
Tasks
- Make cloramphenicol stock. Check.
- Make glycerol stocks of important parts. Discard old plates. Check.
- Perform CFU-assay of lysis induced cells. Check. Redo?
- Combine LuxR-HSL and lysis device.
- Combine pBAD and GFP
- Research lactate production in E. coli
- Write more for the book chapter
- Research QuikChange
Useful links
http://www.nanodrop.com/Support.aspx?Type=Maintenance&Cat=NanoDrop%201000
http://www.troemner.com/pdf/PipetteStandardsHandbook.pdf'
http://www.pipette.com/Support/GuideToPipetting.pdf
https://2008.igem.org/Team:EPF-Lausanne/2-step_PCR
https://2009.igem.org/Team:UNIPV-Pavia/Parts_Characterization#Microplate_reader_experiments
[http://www.jbioleng.org/content/5/1/17 Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits]
[http://www.sbkb.org/tt/ Structural Biology Target Registration Database]
[http://dnasu.asu.edu/DNASU/ DNASU plasmid repository]
[http://www.addgene.org/ Addgene plasmid repository]
[http://plasmid.med.harvard.edu/PLASMID/ PlasmID database]
[http://www.chuq.qc.ca/labomoss/english%20pages/protocols.html Moss lab protocols]
Lactate genes and promoters:
[http://www.biomedcentral.com/1471-2180/10/321#B24 Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate]
[http://aem.asm.org/content/71/10/5920.full Characterization of a Corynebacterium glutamicum Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production†]
[http://www.genome.jp/dbget-bin/www_bget?cgb:cg1027 KEGG: cg1027]
[http://jb.asm.org/content/191/13/4251.abstract The ldhA Gene, Encoding Fermentative l-Lactate Dehydrogenase of Corynebacterium glutamicum, Is under the Control of Positive Feedback Regulation Mediated by LldR
[http://mic.sgmjournals.org/content/142/5/1297 Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif]
[http://www.sciencedirect.com/science/article/pii/S016816560300155X Promoters of Corynebacterium glutamicum]
[http://www.rcsb.org/pdb/explore/explore.do?structureId=2di3 C. glutamicum lldR crystal structure]
RNA polymerase:
[http://www.ncbi.nlm.nih.gov/pubmed/9916034 Oriented, active Escherichia coli RNA polymerase: an atomic force microscope study]
[http://pubs.acs.org/doi/abs/10.1021/jp9071197 Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner]
[http://www.ncbi.nlm.nih.gov/pubmed/10910724 Rapid purification of His(6)-tagged Bacillus subtilis core RNA polymerase]
[http://www.sciencedirect.com/science/article/pii/0092867495903879 Wang et al, 1995: Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex]
DNA oligo and gene synthesis
http://www.invitrogen.com/site/us/en/home/Products-and-Services/Product-Types/Primers-Oligos-Nucleotides/invitrogen-custom-dna-oligos/Technical-Resources-for-Oligonucleotides/DNA-Oligo-FAQ.html#1
PCR
[http://irc.igd.cornell.edu/Protocols/PCR_principles.htm PCR Principles and Practices]
[http://www.neb.com/nebecomm/products/protocol54.asp New England Biolabs: PCR Guidelines]
http://www.uq.edu.au/vdu/PDU_PCRPrimers.htm
[http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html Premier biosoft: PCR primer design guidelines]
http://www.cybertory.org/exercises/primerDesign/index.html
http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/general_pcr_protocol.html
[http://www.miraibio.com/blog/2008/03/10-tips-for-designing-pcr-primers-that-work/ 10 tips for designing PCR primers that work]
[http://www.ehow.com/how_7242346_make-oligonucleotide-primers-pcr.html How to make oligonucleotide primers for PCR]
Software
http://molbiol-tools.ca/molecular_biology_freeware.htm
quorum sensing
[http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.165 Quorum sensing in bacteria - Annu. Rev. Microbiol. 2001. 55:165–99]
[http://www.ncbi.nlm.nih.gov/pubmed/16487323 N-acyl-L-homoserine lactone signal interception by Escherichia coli.]
Other
[http://www.bion.no/2011/11/syntetisk-biologi/ Syntetisk biologi: Genmodifisert bakterie drep annan bakterie]
http://en.wikipedia.org/wiki/DNA_ligase
